ArticleNucleic acids research2013
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers, 1 of them a synthesis that pooled it.
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Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Current computational tools for protein lysine acylation site prediction.Briefings in bioinformatics · 2024Pooled it
- Interplay between NRF2 post-translational modifications and protein-protein interactions: Perspectives from emerging structural and functional evidence.Archives of biochemistry and biophysics · 2026Review
- PMADS: an integrated database of curated and proteomics-inferred associations between protein post-translational modifications and drug sensitivity.Nucleic acids research · 2026Article
- Metabolic and post-translational modifications in sepsis-associated immune dysfunction: a conceptual framework.Frontiers in immunology · 2026Review
- E2-regulated transcriptome complexity revealed by long-read direct RNA sequencing: from isoform discovery to truncated proteins.RNA biology · 2025Article
- PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins.Journal of proteome research · 2025Article
- Click Chemistry Methodology: The Novel Paintbrush of Drug Design.ACS chemical biology · 2025Review
- LMPTMSite: A Platform for PTM Site Prediction in Proteins Leveraging Transformer-Based Protein Language Models.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Frk positively regulates innate antiviral immunity by phosphorylating TBK1.Frontiers in microbiology · 2025Article
- Dissecting the functional behavior of the differentially phosphorylated prolyl isomerase, Pin1.Protein science : a publication of the Protein Society · 2024Article
- Ubiquitination and deubiquitination in the regulation of NJournal of molecular medicine (Berlin, Germany) · 2024Review
- Current status of PTMs structural databases: applications, limitations and prospects.Amino acids · 2022Review
- UNFERTILIZED EMBRYO SAC 12 phosphorylation plays a crucial role in conferring salt tolerance.Plant physiology · 2022Article
- Enhancing the Discovery of Functional Post-Translational Modification Sites with Machine Learning Models - Development, Validation, and Interpretation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The ubiquitin proteoform problem.Current opinion in chemical biology · 2021Review
- A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications.Chemical reviews · 2021Review
- Physiological relevance of post-translational regulation of the spindle assembly checkpoint protein BubR1.Cell & bioscience · 2021Review
- Robust inference of kinase activity using functional networks.Nature communications · 2021Article
- Dysregulation of USP18/FTO/PYCR1 signaling network promotes bladder cancer development and progression.Aging · 2021Article
- Polyphyllin VII suppresses cell proliferation, the cell cycle and cell migration in colorectal cancer.Oncology letters · 2021Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins. The combination of individual PTM states is a key to modulate cellular functions as became evident in a few well-studied proteins. This combinatorial setting, dubbed the PTM code, has been proposed to be extended to whole proteomes in eukaryotes. Although we are still far from deciphering such a complex language, thousands of protein PTM sites are being mapped by high-throughput technologies, thus providing sufficient data for comparative analysis. PTMcode (http://ptmcode.embl.de) aims to compile known and predicted PTM associations to provide a framework that would enable hypothesis-driven experimental or computational analysis of various scales. In its first release, PTMcode provides PTM functional associations of 13 different PTM types within proteins in 8 eukaryotes. They are based on five evidence channels: a literature survey, residue co-evolution, structural proximity, PTMs at the same residue and location within PTM highly enriched protein regions (hotspots). PTMcode is presented as a protein-based searchable database with an interactive web interface providing the context of the co-regulation of nearly 75 000 residues in >10 000 proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.